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Hong Kong (HKSAR) - The Centre for Food Safety (CFS) of the Food and Environmental Hygiene Department (FEHD) today (August 26) announced results of the regular influenza virus surveillance programme on pigs conducted by the University of Hong Kong (HKU) for May to July at the Sheung Shui Slaughterhouse. Among some 1,300 samples tested, no human swine influenza virus (pandemic H1N1) was detected. However, 16 samples taken in June and July were found to contain a virus that was essentially a swine influenza H3N2 virus but had picked up some genes of human swine influenza virus.

A spokesman for the CFS said, "A case of swine influenza H1N1 virus carrying the genes of the human swine influenza virus was also found in the surveillance programme early last year.

There have been reports from many parts of the world showing similar findings."

According to Professor JSM Peiris, the HKU expert in charge of the surveillance programme, it is unlikely that this swine influenza H3N2 virus, which carried the genes of the human swine influenza virus, will cause any major human health risk or problems in food safety.

The spokesman said, "Given the fact that the human swine influenza virus has spread worldwide in humans and pigs have also been infected by this virus, the recent finding is not a cause for surprise. HKU is conducting further tests to learn more about this particular strain.

"The CFS would continue to monitor reports of the HKU surveillance programme and make announcements on a regular basis. Results will be announced immediately if there are significant public health impacts."

Under the regular influenza virus surveillance programme for pigs, the CFS has been helping HKU researchers to collect blood and tracheal and nasal swabs from pigs at the Sheung Shui Slaughterhouse twice a month to monitor influenza virus activity in pigs.

According to the World Health Organization, the World Organisation for Animal Health and the Food and Agriculture Organization of the United Nations, human swine influenza would not be contracted by consuming pork and pork products that are handled properly and thoroughly cooked.

Members of the public are advised that it is safe to eat pork and pork products that are cooked to an internal temperature of 70 degrees Celsius or above.

The CFS spokesman said that all imported live pigs from the Mainland come from registered farms and are accompanied with animal health certificates issued by the Mainland authorities.

"The FEHD inspects the certificates and health of the imported pigs at the boundary control points.

Both imported and local pigs also have to go through ante-mortem and post-mortem inspections in the slaughterhouses. Only pigs that pass the inspections can be supplied to the market and sold for consumption," he said.

Apart from the enhanced inspection of imported live pigs, the FEHD has reminded slaughterhouse staff and people who might be in contact with live pigs to pay attention to personal hygiene and to wear masks and appropriate protective gear at work.

The CFS has been keeping close liaison with the Mainland authorities over any abnormal situation concerning Mainland farms supplying live pigs to Hong Kong, and farm inspection would be stepped up when necessary, the spokesman added.

In addition, the Agriculture, Fisheries and Conservation Department also closely monitors the health situation of pigs in Hong Kong and regularly reminds local pig farmers to maintain good farm and personal hygiene and report to the Department any abnormality in farms.


source:http://www.gov.hk/en/residents/

Recombinomics Commentary 14:20
August 27, 2011
The CDC has released a full set of pandemic H3N2 (trH3N2) sequences (at GISAID) from a toddler (1M) collected July 24, 2011 in Indiana (A/Indiana/08/2011).  The isolate is a reassortant with a pandemic H1N1 MP, which is the first such constellation reported in humans.  Moreover, the PB1 is most closely related to the PB1 from the 2007 Huron County Fair and therefore does not have E618D.

The H3 sequence is closely related to the 2010 human cases (A/Minnesota/11/2010, A/Wisconsin/12/2010, A/Pennsylvania/40/2010, A/Minnesota/09/2010), but is most closely related to two recent swine isolates, including one from Indiana (A/swine/North Carolina/A01049436/2011 and A/swine/Indiana/A0109091/2010).  However, the MP in the two swine isolates are identical, but related to North America swine, which is easily distinguished from the pandemic H1N1 MP in the above case.

The presence of pandemic MP in the recent cases raises concerns a further adapotation of trH3N2 to humans.

The CDC has begun testing a trH3N2 vaccine target, A/Minnesota/11/2010 X-203, which is related to the above case and from a cluster. 

The latest case is not described in the CDC's MMWR or website.  More deatil on those case and symtoms in contacts would be useful.

Recombinomics Commentary 21:40
August 26, 2011
A cluster of oseltamivir-resistant A(H1N1)2009 influenza cases with onset between May and August 2011 has been detected in the Hunter region of New South Wales (NSW), Australia.

Viruses from 25 of 184 (14 percent) A(H1N1)2009 cases from the Hunter
New England region exhibited highly reduced oseltamivir sensitivity
due to the H275Y substitution in the neuraminidase.

15 of the 1st 16 cases lived within a 50-km radius of the regional
centre of Newcastle. 16 of the 25 patients have been interviewed, and
none had received oseltamivir prior to influenza specimen collection.
 
The above comments describe the clonal expansion of H274Y in New South Wales province in Australia.  The WHO regional center in Australia recently released three sequences (A/NEWCASTLE/14/2011, A/NEWCASTLE/47/2011, A/NEWCASTLE/58/20110 from Eleebana, Rutherford, and Cessnock, which are all within 30 km of Newcastle, and collected in June and July by John Hunter Hospital, Virology Unit, Clinical Microbiology in Lambton. 

The HA from these sequences had S188T and all three sequence were identical, but none had H274Y.  However, the identity of all three sequence from the region with H274Y suggests the resistant H1N1 matches the above sequences with H274Y appended to that genetic background. 

These sequences are distinct of the clonal expansion of H274Y in Japan, or Delaware and Maryland, which involve additional S188T sub-clades.  The expansion of multiple sub-clade with S188T and H274Y in three different continents indicates H274Y on an S188T is evolutionary fit and is rapidly spreading via hitchhiking and clonal expansion.

More than two dozen cases of H1N1 swine flu resistant to Roche Holding AG (ROG)’s Tamiflu pill were reported in Australia in the largest outbreak of the drug- evading influenza strain.

Viruses from 25 of 184 patients in the Newcastle area of eastern Australia infected with the pandemic germ had a genetic mutation that reduces the potency of Tamiflu, scientists said in a report distributed today by the International Society for Infectious Diseases’ ProMED-mail program.

The cases, first reported in May, raise concern that the resistant strain may spread, leaving doctors without their preferred treatment for influenza. GlaxoSmithKline Plc (GSK)’s Relenza drug is effective against the mutant strain, which is still found in the Newcastle area, according to the World Health Organization’s Collaborating Centre for Influenza in Melbourne.

“As long as it’s isolated to Newcastle and that region, it’s not so much of a problem,” said Ian Barr, the center’s deputy director, in a telephone interview today. “If it spreads further, it might be a concern. Fortunately, we’re heading toward the end of our flu season.”

The cluster of cases with the mutant virus is the largest reported outbreak globally to date, and shows the new variant is capable of being transmitted efficiently in the absence of drug pressure, said Jennifer McKimm-Breschkin, a virologist at the Commonwealth Science and Industrial Research Organization in Melbourne, who studies antiviral resistance.

‘Fit and Transmissible’

“It’s clearly fit and transmissible,” she said in a telephone interview today. “It would be concerning having seen such a large cluster like that.”

None of those infected had taken Tamiflu prior to being tested for flu. Of 16 patients interviewed by the scientists, none had a history of immune suppression, which contributes to drug resistance. None of the patients was admitted to an intensive care unit or died from the infection, the report said.

Further interviews with cases and virological analyses are ongoing, the scientists said.

The H1N1 virus that emerged in 2009 known as swine flu was reported in more than 214 countries and caused about 18,450 deaths worldwide through August 2010, when the WHO declared an end to the pandemic. It’s since become one of three seasonal flu strains circulating worldwide, causing infections mostly during the winter months.

Sporadic Resistance

Studies have shown that Tamiflu-resistant bugs develop sporadically in 0.4 percent to 4 percent of adults and children treated for seasonal influenza, according to Basel, Switzerland- based Roche.

The outbreak of resistant H1N1 in Newcastle probably emerged in a treated patient who passed the infection onto others, McKimm-Breschkin said.

Ten to 15 percent of H1N1 infections in the Hunter Valley area of New South Wales state, which includes Newcastle, are resistant to Tamiflu, WHO’s Barr said. The seasonal flu vaccine protects against the new flu variant, as well as influenza type B, the main strain circulating in the Newcastle area, he said.

Tamiflu and Relenza, an inhaled powder, reduce the severity and the duration of flu symptoms by 24 to 30 hours if treatment is started within the first two days of illness, according to the companies. Both drugs work by blocking a protein on the surface of influenza particles called neuraminidase, which allows the virus to spread from infected cells to other cells.

Mutant H1N1 viruses evade Tamiflu through a single genetic change known as the H275Y mutation which prevents the medicine from clinging to neuraminidase, enabling the pathogen to spread.

An outbreak of cases of seasonal flu with the H275Y mutation was first recorded by Norway in January 2008 and by the following August widespread resistance was reported in 40 countries in Europe, North and South America, Africa, Asia and Australia.

http://www.bloomberg.com/news/2011-08-25/tamiflu-resistant-flu-outbreak-reported-in-australia-s-newcastle-who-says.html

Recombinomics Commentary 13:30
August 18, 2011
Recently released H1N1 sequences (at GISAID) by the WHO regional center in Australia included a new pandemic H1N1 target, IVR-159 A/Victoria/502/2010.  The HA sequence included Q226R, which was also added to the H1N1 vaccine target being tested by the CDC, A/South Carolina/02/2010. Q226R was not in either original sequence.  This receptor binding domain change increases growth in chicken eggs, and may be grossly under-represented in the GISAID and Genbank sequence databases because most H1N1 isolates are from infections of mammalian cells (MDCK).

The use of MDCK cells reduces the frequency of changes at key HA positions, such as 225 and 226 in the receptor binding domain, as well as positions 156-159 which are involved in immune recognition.  The new CDC vaccine target also had K157E and two way testing using the old and new vaccine targets produced “LOW FAIL” results indicating the anti-sera against the old target, A/California/07/2009, had limited activity against the new target, and anti-sera against the new target had limited activity against the old target.

Last year an egg isolate of A/Victoria/502/2010 had D225G.  The new vaccine target is wild type at position 225, but has Q226R.

The testing of new targets at this time is unusual because at the most recent meetings of the vaccine advisory committee for the US FDA, as well as the WHO meeting, recommended no changes in the three vaccine targets, and that vaccine for the 2011/2012 flu season in the northern hemisphere will be shipping shortly.

The testing of new targets by the CDC and WHO at this time raises serious concerns that the vaccine for the 2011/2012 season will have limited utility.

WHO Testing New Seasonal H3N2 Vaccine Target
Recombinomics Commentary 15:55
August 18, 2011

Recently released H3N2 sequences by the WHO regional center in Australia included a new seasonal H3N2 target, A/Victoria/563/2010 IVR-160.  This sequence follows the release of three H3N2 targets by the CDC, A/Brisbane/11/2010 X197, A/Rhode Island/01/2010 X-199, and A/Perth/10/2010 X-207.  These four targets are being tested as a replacement for the current H3N2 target, A/Perth/16/2009.

The testing of new targets at this time is unusual because at the most recent meetings of the vaccine advisory committees for the US FDA, as well as the WHO meeting, the committees recommended no changes in the three vaccine targets, and that vaccine for the 2011/2012 flu season in the northern hemisphere will be shipping shortly.

The testing of new targets (seasonal H3N2, pandemic H1N1, and influenza B) by the CDC and WHO at this time raises serious concerns that the vaccine for the 2011/2012 season will have limited utility. 

Recombinomics Commentary 18:30
August 17, 2011
The CDC has released another series of 2011 H1N1 sequences.  Included was A/Mexico/2058/2011 from a 36M collected on March 15, 2011.  The age, gender, and collection date match an earlier case which was associated with another sequence, A/Mexico/DRE1945/2011.  However, it is unclear why sequences from the same patient would be given different numbers.  The March 15 was a week earlier than subsequent collections, strongly suggesting that Mexico/2058 and Mexico/DRE1945 are from the first confirmed cases in Chihuahua from the Chihuahua sub-clade.

The sequences from the National Labs contained D225N, which was stated in the title of the associated characterization sheet, “Detection of D222N substitution in Pandemic Influenza A (H1N1) Virus in Chihuahua, Mexico”.  The CDC sequence was from an egg isolate, and was closely related to the earlier sequence, but had D225G, raising concerns that the frequency of D225G is grossly under-reported because most isolates are from MDCK cells which select against D225G.

The sequence from the lab in Mexico was direct and from a sample from the upper respiratory tract and was not reported as a mixture.  Similarly, the CDC sequence was from an egg isolate, and also not reported as a mixture, although the age, gender, and collection date indicate both sequences were from the first confirmed case, which was fatal and from the partner of another fatal case, who had similar symptoms, but isolation attempts failed.  The linkage of these two fatal cases, as well as additional severe and fatal cases from the same traffic patrol office led to a WHO pandemic alert.

The time delay, and egg isolation raises concerns that there are many more sequences from Chihuahua with D225G and D225N, which would provide more linkage to severe and fatal H1N1 cases, as indicated in multiple anecdotal reports.  Similarly, the detection of D225G in an egg isolate raises concerns that the H1N1 sequence database in general grossly underestimates the frequency of D225G and D225N in severe and fatal cases since most sequences are from isolates grown in mammalian MDCK cells.

The changes in positions 225 and 226, as well as positions 156-159 are important because they are associated with immunological escape, as well as targeting of human lung.  Both human lung and chicken embryos in eggs, are rich in gal 2,3 receptors.

The heavy use of MDCK would also produce a gross undercount in low reactors, which led to the recent recommendation to leave all three vaccine targets unchanged in spite of record high fatality rates in pneumonia and influenza (P&I) patients.  These concerns are likely linked to the recent sequences for new vaccine targets.  The latest, A/Victoria/502/2010, was just released by the WHO regional center in Australia.  Like the new pandemic H1N1 target released by the CDC, it has Q226R.  The initial egg isolate from this patient had D225G, while an MDCK isolate was wild type at positions 225 and 226.  These new vaccine target raise concerns that the current vaccine in use in the southern hemisphere, as well as the vaccine shipping for the 2011/2012 season in the northern hemisphere, will have limited utility.

Submitted by Deepti Rajan on Fri, 08/12/2011 - 11:57

Southern states of Kerala and Karnataka are finding it difficult to get rid of the H1N1 virus, with 16 new deaths reported from the two states in June and July.

According to central government figures, Kerala reported 174 cases of confirmed H1N1 infections in the two months, while Karnataka reported 34 infections. None of the other states reported such outbreaks during the period.

The fatality rate was higher in Karnataka, with 6 deaths out of the 34 cases or roughly one six (18%), much higher than the death-rate during the height of the pandemic in 2009. At that time, the death rate was just 5.7%.

Kerala reported 8 deaths among 174 infections during the two months, a fatality rate of 4.6%. This too was mildly above the long term fatality rate of 3.9% in the state. The national long-term average is 5.9%.

The risk of death due to H1N1 increases during 'off peak' times as people are not on their guard against the pandemic and tend to mistake the infection for ordinary flu. The symptoms of H1N1 are very similar to a normal cold and many people never realize that they have had it.

It is particularly fatal to people with weak immune systems, such as pregnant women, TB patients, malnourished people etc..

With these, the death toll from the H1N1 in Kerala has risen to 129 and to 255 in Karnataka and to 2,772 nationally.

Total confirmed infections have risen to 46,777 by the end of July.

The H1N1 virus spread to India from foreign countries and particularly affected the regions that send a large number of migrant workers abroad, such as Kerala.

Altogether, the prevalence of the virus was much higher among the Western states of India, which tend to be more connected to the rest of the World, than the interior or the East.

Leading the toll was Maharashtra with 34% of all deaths in India, not least because of Mumbai, followed by Gujarat, with roughly half the number of deaths.

They were followed by their northern neighbour Rajasthan and southern neighbour Karnataka.

http://rtn.asia/920_h1n1-swine-flu-refuses-die-down-kerala-karnataka-16-dead-2-months

Recombinomics Commentary 20:30
August 6, 2011
The two cases from Minnesota occurred in a father (index case) and child. The fatherhad a nasopharyngeal swab positive for swine-origin influenza A (H3N2) virus and had direct swine exposure 6 days before illness onset. The child, whose infection with influenza A (H3N2) virus was confirmed several weeks later by serologic testing, did not have direct swine exposure, and most likely acquired infection from close contact with her father. Other persons in the same household also had ILI during the same period, but serologic results were either negative or inconclusive.
   
The above description of the Minnesota trH3N2 cluster highlights detection and reporting problems associated with trH3N2 cases.  Yesterday’s week 30 MMWR reported a second trH3N2 cases in 2011, and it is likely that the reported cases was the daughter described above (who was infected in 2010 but not reported until in 2011.  The above report was from week 21 MMWR and the case was confirmed by serological testing.  It is likely that virus was isolated recently, leading to the report of the second cases in 2011.  This confirmation may have also led to the use of the isolate from the index case as the pandemic H3N2 (trH3N2) vaccine target.

Like the first cases reported in 2011, the index case’s daughter was not hospitalized and the lab confirmation was difficult.  The other 2011 case was from a September 6, 2010 infection that was reported in week 4 of 2011.  Two of the three late 2010 infections that were reported in 2010 were from hospitalized cases, which were more likely to be tested beyond a rapid test or a serotype test, both of which would suggest the trH3N2 cases were seasonal H3N2, because trH3N2 has a human H3 and N2 from the 1990’s.  Thus, these samples could be detected in a H3 serological test, although the signal may be low, and many cases would be unsubtypable, as reported by Pennsylvania where two of the confirmed cases were located (A/Pennsylvania/40/2010 and A/Pennsylvania/14/2010).

The delayed reporting for the above two 2010 cases is similar to reporting for the 2009 Iowa case (A/Iowa/16/2009), which was from a September infection that was analyzed in November and reported in January, 2010.  These delayed cases not only were reported in the year after infection, but infections were early in the season, prior to the large influx of seasonal cases which would have decreased the likelihood of the more extensive testing, which is required for the detection of trH3N2.

The genetic similarities seen in the human cases suggests the number of cases is much higher than the small number of reported cases and it is likely that the number of cases being investigated is significantly higher than the two cases cited in the 2011 week 30 MMWR, which are likely to be cases infected in 2010.

Recombinomics Commentary 14:30
August 6, 2011
The two cases from Minnesota occurred in a father (index case) and child. The fatherhad a nasopharyngeal swab positive for swine-origin influenza A (H3N2) virus and had direct swine exposure 6 days before illness onset. The child, whose infection with influenza A (H3N2) virus was confirmed several weeks later by serologic testing, did not have direct swine exposure, and most likely acquired infection from close contact with her father. Other persons in the same household also had ILI during the same period, but serologic results were either negative or inconclusive.

The above comments are from an update of influenza activity in the US (in week 21 MMWR).  This week the CDC released sequences from the index case (initially decibed here and discussed here and here) in a construct for a trH3N2 (pandemic H3N2) vaccine from the index case (31M) described above, A/Minnesota/11/2010. The sequences from the index case represented a reassortant, with an H3 closely related to recent trH3N2 sequences (A/Wisconsin/12/2010, A/Pennsylvania/40/2010, A/Minnesota/09/2010), and an N2 distantly related to A/Pennsylvania/14/2010.  Most internal genes are closely related to WI/12 and PA/40 which were collected within days of each other and are closely related to each other.

The above Minnesota cluster includes additional family members with ILI (influenza-like illness) as was seen in initial pandemic H1N1 clusters in California in 2009.  The second trH3N2 reported in this week’s MMWR may represent an isolate from the Minnesota cluster.

It is likely that the number of trH3N2 cases in the United States is far higher than the confirmed / reported cases. 

More detail on trH3N2 cases under investigation would be useful.

Recombinomics Commentary 18:05
August 4, 2011

the two cases reported during 2011, were identified as swine influenza A (H3N2) virus
 
The above comments, from the week 30 MMWR footnote confirm that the novel influenza case reported in the MMWR preview was trH3n2 (pandemic H3N2), but the footnote does not provide any additional information.  The first case reported in 2011 was a case (3F) from Pennsylvania (A/Pennsylvania/40/2010) from a sample collected September 13, 2010.  Thus, it is unclear when the second reported case was infected, and the sequence has not been released, so the relation to the other case reported in 2011 is unclear.

The above case (3F) was infected close to the date of a Wisconsin (A/Wisconsin/12/2010) case (10 month M) who developed symptoms on September 8, 2010, and was announced in a pager alert.  The sequences were closely related, raising concerns the cases in Wisconsin and Pennsylvania signaled human transmission, since there was no reported contact between these cases raising concerns of a large number of unrelated cases. 

These concerns were increased by the second case (31M) from Minnesota (A/Minnesota/11/2010) which was collected on November, 29, 2010 but was closely related to the cases in Wisconsin and Pennsylvania.  Low levels of human transmission would not be easily detected because trH3N2 has human H3 and N2 from the mid-1990’s so serotyping reagents would give results similar to seasonal flu and not indicate a need for further testing, like antigen characterization or sequencing, which would be done at the CDC.

Thus, like the first reported case in 2011, the second 2011 could have been collected months earlier.  Moreover, recent sequences from the CDC came from virus isolated in eggs, which would increase the detection of trH3N2 because of D225G, which is a change that increases affinity for gal 2,3 receptors which are found in eggs, as well as human lung.

Yesterday the CDC released sequences associated with the development of vaccine targets. Included were sequences from the Minnesota case, raising concerns that the number of suspect or confirmed trH3N2 cases in 2011 is significantly greater than the two reported cases.

Additional information, including sequence data on the latest reported case would be useful, as would additional information on other confirmed or suspect trH3N2 cases.

Recombinomics Commentary 15:30
July 21, 2011
The flu vaccine for the upcoming season should trigger some déjà vu: The formulation will be identical to last year’s, the Food and Drug Administration has announced.

The above comments once again raise serious concerns about the lab manipulated data used to select influenza vaccine targets.  In 2011 the US Pneumonia and Influenza (P&I) death rate was a record levels which were similar to rates in 2008.  In 2008 the vaccine mismatches for all three targets was acknowledge and all three were changed for the 2008/2009 season in the northern hemisphere.  In 2011 the clear mismatches were denied and as indicated above, the targets for the 2011/2012 season remained unchanged.

These decisions are largely dependent on the anigen characterization tests which test new influenza isolates against antisera directed against the current vaccine targets.  This assay can be heavily manipulate at both ends of the assay, the creation of reference antisera as well as the procedures for the isolation of virus from new infections.

Sequence data has revealed dramatic inconsistencies in the assays, where identical sequences can signal the presence or absence of low reactors (isolates that reduce the titer 4 fold or more).  The data for pandemic H1N1 has been striking, in part because of a significant increase in public H1N1 sequences coupled with a target that has remained unchanged since the first target was selected in the spring of 2009.  The H1N1 has clearly evolved away from the initial sequences leading to more severe outbreaks in countries which were subjected to significant outbreaks in the prior season.

The detection of low reactors has been strongly linked to changes at positions 157-160 which have repeatedly produced high frequencies of low reactors, especially in more recent isolates.  However, changes at these positions as well as receptor binding domain changes are heavily dependent on virus isolation procedures.  Moreover, such changes can also target gal 2,3 receptors present in chicken eggs as well as human lung.  Virus isolation using mammalian cells rich in gal 2,6 receptors can select away from the changes that create low reactor results and target human lung, but such isolates are used to justify continued use of the older targets.

This bias, as well as under-reporting of H1N1 due to a lack of testing or use of the intensity “rapid test" is somewhat limited in the pneumonia and influenza death rate, which does not require lab confirmation.  This rate also signals immunological escape which leads to more infections and deaths.  Thus, the high death rate in 2011, like the similar rate in 2008, signals a need to change the vaccine targets.  The failure to change any of the targets for the 2011/2012 raises serious questions about the assays and consultants used by the FDA and WHO in the selection of targets, which this season were unchanged by committees representing most agencies.  Thus, the worldwide targets for the 2011/2012 season are the same and unchanged from the prior season (and the H1N1 target is the same as 2009, A/California/07/2009).

The latest FDA approval once again indicates that an independent scientific review of the committees and procedures associated with influenza vaccine target selection is long overdue.

Recombinomics Commentary 23:55
July 1, 2011
Today NIID released 37 HA sequences from 2011 (at GISAID), which were associated with frequent Tamifu resistance (H274Y) in most associated NA sequences, as well as one NA sequence with S246N, signaling additional clonal expansion. 

However, the HA sequences had an alarming number of changes at positions 156-159, with 6,1,9,2 changes respectively.  The prior data on 33 HA sequences from Japan had postion 156-159 chnages of 1,3,5,1, respectively. Changes at these positions are linked to low reactors which have titers reduced four fold or more when tested against the current H1N1 vaccine target, A/California/07/2009.  These numbers are likely to represent an underestimate because the isolates involved growth on mammalian MDCK cells, which are rich in gal 2,6 gal.  Isolation with eggs, which are rich in 2,3 gal receptors would have selected addition examples of changes at this position.  These changes are biologically and clinically relevant because they are associated with vaccine escape as well as preferential growth in human lung, which is rich in gal 2,3 receptors.

The changes are increasing in prevalence, but these alarming changes are being discounted with claims that the changes are artifacts of culture since detection is more difficult in direct sequencing of clinical samples since the changes are frequently present as mixtures with wild type.

The discounting of these changes has significant consequences.  In the United States Pneumonia and Influenza (P&I) deaths were at record levels in 2011 and were similar to rates recorded in 2008.  However, in 2008 the vaccine mismatches with all three vaccine target were eventually acknowledged and all three targets were updated for the following season.  In contrast, in 2011 claims were made that all three targets were “matches” due in part to extensive manipulation of laboratory test results, including claims that negative data invalidated positive data.  Consequently, all three vaccine targets remained unchanged for the 2011/2012 season.

In addition to the elevated P&I death rate, the frequency of Tamiflu resistance has also increased and significant clonal expansion has been seen in the United States and Japan for H274Y.  The reported numbers are underestimates because WHO collaborating centers have agreed to not report Tamiflu resistance when H274Y levels are less than 50% of the sample signal. In addition, clonal expansion of Tamiflu and Relenza resistance (S246N) has been reported in Singapore and Australia, including 30% of H1N1 isolates from Darwin.

These increases in low reactors as well as Tamiflu resistance highlight the folly of lab manipulations to generate under-estimates for “scientific” public reports published by government and international agencies, and these policies and publications remain hazardous to the world’s health.

Recombinomics Commentary 14:30
June 30, 2011
The recent comments on detection of multiple neuraminidase resistance markers (S246N with H274Y or I222R) has increased concerns that such markers are more prevalent than reported.  This concern was increased by the failure of the CDC to release sequences from recent Delaware H1N1 isolates with H274Y. 

Earlier this season the CDC released four 2011 sequences from Delaware and four from Maryland and all eight sequences had H274Y.  All eight sequences were collected in February or March and represent the eight most recent isolates from these two states.  Phylogenetic analysis indicated H274Y was spreading via recombination and clonal expansion.  One of the sequences, A/Maryland/04/2011, was from the Chihuahua sub-clade, while the other seven were from the S188T sub-clade.  The first three sequences from Delaware had A189T, signaling clonal expansion.  Moreover, the fourth Delaware sequence, A/Delaware/08/2011, was virtually identical to A/Maryland/06/2011, signaling additional clonal expansion.  The H274Y was discovered through routine surveillance and was not linked to Tamiflu treatment raising concerns that the detection of H274Y in all eight of the most recent isolates from Delaware or Maryland signaled the start of significant spread of H274Y.
 
These concerns were increased when Delaware announced ten additional cases with H274Y, as determined by the CDC, supporting significant spread.  However, the recently released H1N1 sequences generated by the CDC did not include any of these ten samples or any additional samples from Delaware.  Similarly, the recently released sequences did not include any samples from new patients in Maryland.  The only Maryland sequence was an egg isolate of Maryland/04/2011 (which also had H274Y).  thus, although all eight of the most recent isolates from Maryland and Delaware, the CDC failed to release any additional 2011 sequences from any new patients, even though Delaware had announced that then CDC had confirmed 10 additional cases.

The withholding of these sequences by the CDC continues to increase pandemic concerns and evidence supporting the fixing of H274Y Tamiflu resistance in pandemic H1N1.

Recombinomics Commentary 14:30
June 30, 2011
But researchers from the WHO Collaborating Centre for Reference and Research on Influenza found that 30 per cent of H1N1 samples collected in Darwin and 10 per cent in Singapore, had the mutation S247N. This variant has lower resistance to current drugs, Tamiflu and Relenza.

Deputy director of the WHO Centre and senior author of the study, Dr Ian Barr, said the mutation was worrying.

"We'd prefer our viruses be completely susceptible to all our medications, so, it's always a concern when we see even low-level resistance to them in these viruses," he said.

Dr Barr said treatments generally would work against the new flu strain, but the greatest problem would be treating patients with more than one type of mutated virus.

A sample from a Perth patient who died in March revealed he had the new S247N mutation, but also another variant, H275Y, a combination 6000 times more resistant than the 2009 pandemic strain.

The above comments raise concerns that additional evidence of S246N in associate with H274Y (Tamiflu resistance) or I222R (Relenza resistance) has been identified following the Eurosurveillance report detailing the clonal expansion of S246N in Singapore and Australia as noted above, as well as the detection of S246N and H274Y in a sample, A/Perth/29/2011, collected five days after the start of Tamiflu resistance.

The rapid appearance of H274Y raises concerns that the H274Y was present prior to treatment.  The report does not mention collections of samples at earlier time points, leaving open the possibility that H274Y was readily detected hours after the start of treatment.  This possibility could be addressed by aggressively cloning the sample collected prior to treatment.  Sequence analysis of several hundred clones from the original sample would address the level of H274Y in the sample prior to treatment.

The evidence for H274Y in the area comes from multiple reports.  One of the first isolates from Singapore was initially wild type and was H274Y positive two days after the start of Tamiflu treatment, again signaling the presence of H274Y as a mixture prior to treatment (and as the dominant species shortly after the start of treatment).  Similarly, reports from Vietnam described the clonal expansion of H274Y in train passengers, and H274Y has been reported in routine surveillance of samples from patients in Thailand.  Moreover, the only other reported sample with S246N and H274Y was from another Australian patient treated with Tamiflu, A/Victoria/2139/2009.

The true level of H274Y in the region is under-reported because most samples are collected prior to Tamiflu treatment and WHO collaborating labs have “agreed” to not report H274Y in samples where the level is less than 50%.  Thus, even when H274Y is detected as a minor species, the sample is reported as wild type (Tamiflu sensitive).

Thus, the latest comments may reflect additional data linking S246N and H274Y to samples collected prior to Tamiflu treatment.  Similarly, the Eurosurveillance paper did not discuss sequences on samples collected at autopsy.  The fatal case with S246N and H274Y was also treated with intravenous Zinamivir (Relenza) raising the possibility that detectable I222R was present at autopsy.

An update on the current situation (the Eurosurveillance report did not cover samples collected after March, 2011) regarding the detection of H274Y and/or I222R in association with the clonally expanding sub-clade with S246N is overdue.

By Nadia Fazlulhaq

Hospitals are full of patients, both young and old, suffering from viral fever with symptoms similar to dengue.

Officials said they were treating more than 150 fever patients a day in all major hospitals including the National Hospital and the Colombo South Teaching Hospital.

Infectious Diseases Hospital’s Consultant Physician Dr. Ananda Wijewickrema said the viral fever epidemic was not life-threatening but could weaken the patient.

“Most of the patients are suffering from vomiting, nausea, diarrhoea and loss of appetite. Therefore it’s important to give them nutritious fluids like king-coconut water, soups and cunjee but carbonated drinks should be avoided,” he said.

According to Dr. Wijewickrema, the viral fever normally lasts four to five days and patients suffer headaches, body aches and joint pains. “It is difficult to differentiate viral fever from dengue. Even the blood tests show similar results. Only paracetamol is recommended when a patient is being treated at home but if fever, severe vomiting and diarrhoea or pain in the stomach persists it’s important to seek treatment from a qualified medical professional,” he said.

It is believed the fever is transmitted from humans to humans through airborne particles that contain the virus, touching contaminated surfaces and sharing food and utensils with an infected person and also through contaminated food and water.

Dr. Roshan Marambahewa, a medical officer attached to the paediatric ward of the IDH, said there had been an increase in the number of children being admitted to the hospital. “Most children are suffering from fever and dehydration resulting in severe vomiting, loss of appetite and not passing urine,” he said.

http://www.sundaytimes.lk/110626/News/nws_05.html

The Medical Research Institute (MRI) said yesterday it was testing blood samples to identify the viral flu strain which was rapidly spreading throughout the country.

The MRI, one of the chief medical institutions which determine the root cause and prevention of illnesses said so far only common influenza germs had been detected in samples checked so far.

“We have a surveillance network through which we are trying to detect what the virus is. So far we have not detected anything abnormal. However if a person is suspected of having the viral flu they should be treated at a hospital,” MRI Director Anil Samaranayake said and added that the viral flu could be connected to the seasonal influenza which appears annually.

Meanwhile the Colombo Municipality said it was possible that most of patients who had been diagnosed as suffering from dengue might have caught the fast spreading viral flu.

The Municipality’s Chief Medical Officer Pradeep Kariyawasam said there had been 1,477 patients suspected to be suffering from dengue in Colombo but on examining the diagnosis card of each patient it was found that only 769 patients had been confirmed cases of dengue.

He said this could mean that the majority might have contracted some kind of viral flu.

“The viral flu and dengue symptoms appear to be similar, and this makes it hard to distinguish one from the other. Nausea, vomiting, headache, a low platelet count, inability to urinate, poor eye sight are some of the common symptoms for both illnesses,” Dr. Kariyawasam said.

He said the 475 confirmed cases of dengue reported this month was an all time high.

Doctors had warned that children were more likely to contract the virus and parents were advised that in either cases of viral flu or dengue it was best to seek hospital treatment.

Meanwhile Colombo school officials said they were not aware of the viral flu that was reported to be spreading especially among children.

Ananda College Deputy Principal, Sampath Weragoda said although some students had been suspected of having dengue the school authorities were unaware of the mysterious viral flu.

“We haven’t detected any kind of threat from the virus will take precautions depending on the prevailing situation,” Mr. Weragoda said.

Royal College Principal Upali Gunasekara said he had not received reports or complaints about the virus. Museus College Principal S. Dandeniya said she was also not aware of a viral flu spreading among children. (Olindhi Jayasundere )

http://www.dailymirror.lk/news/12098-mri-testing-blood-samples-to-identify-viral-strain.html

Recombinomics Commentary 12:00
June 21, 2011
Based on available data, among Japanese oseltamivir resistant viruses, the vast majority were from cases treated or prophylaxed with oseltamivir.

The recently release sequences by the US CDC and Japan’s NIID provided clear examples of H274Y (oseltamivir / Tamiflu resistance) clonal expansion in the United States and Japan.  The US isolates were geographically clustered in Delaware and Maryland, with four isolates each.  These isolates formed small clusters of clonally expanding H274Y.  Seven of the eight were in the S188T sub-clade.  The first three isolates from Delaware had A189T appended onto this background.  A189T is the receptor binding domain change in the Chihuahua sub-clade and the only public Chihuahua sequence with H274Y is also in Maryland.  Thus, the US sequences demonstrated the movement of H274Y onto geographically clustered genetic backgrounds due to recombination driven by a high concentration of H274Y.

The sequences from Japan represented the converse situation, where the same sub-clade, which was also S188T, had spread throughout the country.  This sub-clade had A200T appended onto the S188T background and 10 fo the 13 sequences for a branch which was exclusively populated by sequences with H274Y.  This expansion and distribution closely mirrored the spread of H274Y in seasonal H1N1, where H274Y was in clade 2B (represented by Brisbane/59/2007) and most isolates were closely related and matched the initial sequences from northern Europe, but H274Y was also present in smaller clusters which were clade 2B, but slightly different than the larger cluster, reflecting additional recombination leading the spread of H274Y in closely related sub-clades.

The striking parallels between H274Y spread in seasonal H1N1 in 2008 and pandemic H1N1 in 2011 strongly suggests that H274Y will soon become fixed in pandemic H1N1.  Like 2008, the spread is driven by clonal expansion and not selection through Tamiflu treatment, which is why the latest comment by WHO on sequences in Japan is cause for concern.  The clear clonal expansion is ignored in the WHO update, and instead reference is made to a linkage between the detection of H274Y and use of Tamiflu by the corresponding patients.  This disconnect between the sequence data and the WHO announcement raises serious competency concerns regarding those responsible for this conclusion / announcement.

The lessons learned from the fixing of H274Y in seasonal H1N1 were clear and the failure to relate this pattern to pandemic H1N1 is alarming.

An explanation by WHO of the data and rationale behind their bizarre announcement (stated above) is needed, along with an independent scientific investigation of  the underlying data and personnel responsible for this gross misinterpretation or misleading comment linked to very clear cut sequence data.

Recombinomics Commentary 14:00
June 20, 2011
Based on available data, among Japanese oseltamivir resistant viruses, the vast majority were from cases treated or prophylaxed with oseltamivir.

The recently released H1N1 sequences from Japan clearly demonstrate the spread of oseltamivir resistance (H274Y) via clonal expansion.  10 of the 13 sequences with H274Y were closely related and mapped to a branch that had no isolates without H274Y.  Moreover one additional sequence, A/Kagawa/2/2011, was closely related and was on an adjacent branch with one isolate, A/Shiga/35/2011, that did not have H274Y.  One of the other isolates with H274Y, A/Iwate/1008/2011, was related to other sequences from Japan, while the other H274Y positive sequence, A/Hiroshima/45/2011, was related to US S188T sequences. 

Thus, 12 of the 13 sequences were from 2011 (representing 38.7% of the 2011 sequences released by NIID) and the vast majority were spreading via clonal expansion, contracting the above quote in the most recent WHO update on H247Y in pandemic H1N1.

This pattern, which included a dominant sub-clade with H274Y, as well as additional examples of H274Y in the same sub-clade but on a distinct background, faithfully matches the pattern of H274Y in seasonal H1N1 in early 2008, which led to the fixing of H274Y in late 2008.  In seasonal flu the pattern was independent of Tamiflu usage.  H274Y was in patients who were not taking Tamiflu as well as countries where Tamiflu usage for treatment of seasonal H1n1 was minimal.

Thus, although the sequence data clearly demonstrates a pattern of clonal expansion of H274Y in pandemic H1N1 in Japan in 2011, the latest WHO report claims that such samples are from patients linked to Tamiflu usage.  Since the expansion pattern covers the entire country and is clonal in nature, and the clone does not contain H274Y sensitive isolates, the WHO comments represent a glaring inconsistency.

The inconstancy is another example of WHO comments which are not supported by the sequence data generated by WHO affiliated labs, and like labs worldwide, describe the rapid appearance of H274Y in parients treated with Tamiflu,  The short time frame between the start of treatment and the detection of H274Y signals spread via an H274Y mixture.  The level of H274Y has now increased so the clonal expansion is clear, as is the lack of a requirement of Tamiflu treatement for the detection of this spread.

The remarkable parallels of the pattern in H274Y spread in seasonal H1N1 in 2008, and pandemic H1N1 in Japan in 2011 strongly predicts the fixing of H274Y in pandemic H1N1 in the near term.

Moreover, the WHO statement on the linkage to Tamiflu use represents a profound failure to communicate this clear clonal pattern that is not linked to Tamiflu usage, and raises significant competency concerns regarding the analysis of the evolution of pandemic H1N1 by WHO consultants and communicators.

Recombinomics Commentary 16:40
June 19, 2011
Based on available data, among Japanese oseltamivir resistant viruses, the vast majority were from cases treated or prophylaxed with oseltamivir.

The above comments from the latest WHO report on oseltamivir (Tamiflu) resiistance in H1N1 implies that the increasing frequency of Tamiflu resistance (H274Y) reported in Japan is due to Tamiflu treatment, but the latest sequences released by Japan’s National Institute on Infectious Diseases (NIID) indicate H274Y increases are due to community clonal expansion across the entire country.

NIID has recently released 43 NA sequences collected between Dec 2, 2010 and Feb 2, 2011.  13 of these sequences (largely from Jan collections) had H274Y and this high frequency (30.2%) may be markedly above the reported 1.5% due to selection of samples for sequencing, but the published sequences clearly demonstrate clonal expansion because 10 of the 13 sequences are virtually identical to each other and form a phylogenetic branch which is exclusively populated by isolates with H274Y,  Moreover, as seen by the list (below) of these 10 isolates, they are from eight different prefectures, indicating the community clonal expansion has spread throughout the country.  This spread is supported by the spike in the detection frequency (to 4.8% in Feb and 5.8% in Mar), which would again be linked to clonal expansion and not linked to Tamiflu treatment (Table 1):

Thus, the basis for the WHO statement remains unclear.  WHO consultants have agreed to report mixtures containing resistant sequences as wild type if the level of H274Y is below 50%, and therefore collection of samples after treatment may increase the level to more than 50%, leading to a resistance (H274Y) positive report. However, the virtual identity of the sequences from the 10 isolates below indicates the spread is via clonal expansion and not “spontaneous” mutations selected by Tamiflu treatment, as implied in the WHO statement above.  Similarly, the wording of the WHO statement leaves open the possibility the patients were treated with Tamiflu after collection of the sample (which is common), and the classification of such patients as "Tamiflu treated" just adds to the confusion created by the “agreement” by consultants to not report Tamiflu resistance in samples where H274Y is below 50%.
 
In either case, the comments by WHO are grossly misleading and are little more than propaganda masquerading as science, creating the illusion that the increasing frequency of H274Y in community cases is linked to spontaneous mutations selected by Tamiflu use, rather than clonal expansion of a dominant sub-clade with H274Y.

A WHO explanation of these misleading reports is long overdue.

Closely related H274Y positive sequences:

A/HIROSHIMA/17/2011
A/WAKAYAMA/23/2011
A/SAPPORO/19/2011
A/NIIGATA/51/2011
A/HOKKAIDO/12/2011
A/YOKOHAMA/29/2011
A/NIIGATA/62/2011
A/KOBE/537/2011
A/YAMAGUCHI/35/2010
A/HIROSHIMA/49/2011